Both players are clear to resume football after the results, with the first player approved for a return to action last Wednesday.
Due to the casual nature of the contact between the second player and his teammates, the FAI permitted the club to return to training on Thursday.
They drew 0-0 with Cork City at the RSC on Saturday afternoon.
"All club activity will now be restored," said Waterford in a statement on social media.
"Waterford FC remains committed to ensuring the safety of staff and the wider public, and will continue to adhere to the strict protocols laid down by the FAI, HSE, and our own Covid-19 team."
"The FAI has urged SSE Airtricity League clubs to continue to follow the FAI Safer Return to Play Protocol and HSE Covid-19 guidelines," read a statement from the Association.